Sonic chronos Shadow's story
by silverofaheartless
Summary: as the world is thretened once more, the timelines clash as heroes from an erased timeline fight once more together to battle like never before, friends fight to collect the emeralds before the enemy but who is the enemy? made as a gameline story
1. Break in

Shadow part in the game story I have been challenged to create.

OMEGA has gone array a familiar yet unfamiliar hedgehog has somehow gotten the best of shadow, the story begins

* * *

Chapter one:Break In

The lone figure watched the whirling waters from a dock, he felt the calm air and envied it as it blew through his dark spines. The dock creaked behind him as another figure joined him. "Shadow"

The hedgehog looked over his shoulder with his same angry scowl he always wore but it immediately softened slightly. Rouge walked up to him holding two cones of ice cream they were both white but one had a cherry on top.

"Here, its good" she said happily insisting he take the one with the cherry, he turned to the bat a brow raised. "What is this?"

"What do you mean what is it?" she said teasingly, "its ice cream" she put it in his hand and he stared at it. She sighed tapping her foot, he looked at her an annoyed look on his face. "Don't give me that look, at least try it"

He snorted, "I don't need to eat my body needs no nutrients, you already know that" She frowned "ya but it doesn't hurt to try, right? Please." He looked at rouge that had a sad look on her face. "It's sweet so it should taste good" she pointed out as she walked paste and sat on the end of the dock looking out at the setting sun.

"And besides sweet beats sour" she liked her cone; he turned and faced the horizon. "And shadow" she looked at him, he kept his gaze up. "You are a very sour apple, so eat it." She joked looking back out over the water, shadow frowned he didn't like making her unhappy but it stung even more when she used him as a target to make herself happy again, it usually involved her silver tongue. He looked at the ice cream and sighed, It won't kill me right, he thought hesitantly he took a simple lick and scrunched his nose up making a face as thought he'd bitten into an lemon, Rouge looked at him and laughed.

"Maybe vanilla isn't your flavour." He sighed heavily and looked at her about to retort but his G.U.N. communicator on his wrist began to beep. Lucky, he thought as he gave rouge the ice cream and activated the tiny communication watch.

"Shadow here" he spoke to the machine, "agent shadow, this is the commander you and rouge need to get back immediately we have an emergency" Shadow frowned, rouge was up and she had already disposed of the two ice creams. "What is the emergency sir?"

"The team that headed to moon rock cavern has gone missing, you will gain more information when you get here" Shadow nodded to himself, rouge looked at him worriedly. "Wasn't omega part of that squad?"

He held his hand out, she frowned at the thought and knew that if shadow was intending to get there immediately then he was also worried. She handed him the red chaos emerald and he put his hand on her shoulder as he uttered the words "chaos control" everything became a blur, when it settled they were in the control room of the GUN base in Westopolis. The commander seemed to be expecting this so was not surprised like some of the other members in the room, he watched as shadow and rouge saluted then became eased once more.

"This is moon rock cavern" the commander began pointing to the large screens, a black stoned cliff face shown with an opening in it. "We had repeated complaints of some group causing trouble in this cave and so we sent a team there but we haven't heard from them for 43 hours since they've entered the cavern" Shadow frowned. "What about before was there any activity before you lost contact?"

"Yes, but you won't like it" the commander went to one of the desks and picked a small object up he clicked a button and a brisk hiss came from it, "malfunctioning I repeat E...ega is Malfun...." there was loud firing in the background then a scream then silence. Shadow closed his eyes, rouge came forward. "The-there's got to be an explanation! I-I mean Omega wouldn't attack agents unless he saw a threat" the commander placed the object down once again then got in his normal stance.

"You forget rouge, he is a machine and can malfunction, if he was tinkered with and programmed to attack us then he will..." Rouge swung her hand around in front of her face carelessly. "He wouldn't let anyone but I or shadows to do that because he trusts us so don't say that" the commander sighed.

"Did you check the cave?" shadow finally spoke breaking the tension in the silence. "Yes all the agents are alive but in critical condition, we'll have to wait for them to wake up to hear the whole story or perhaps" The whole room went dark and the lights flashed red. "INTRUDERT ALERT, INTRUDER ALERT SECTION 23" the system spoke in a robotic voice, shadow looked at the commander who gave a nod, and shadow disappeared in a flash.

"Come on, come on!" shadow reappeared in a flash of green, a strong force threw him into the wall. "Sorry chaos" the voice was familiar in a way a dark blue blur flew bye. Shadow felt fumbled for a moment but was pulled up, "Shadow, shadow you're the only one fast enough to catch that thing go!" he looked at who had him a G.U.N. grunt was helping him up while two others were catching their breath. Shadow shook his head and nodded to the grunt, he jerked forward and began chasing the intruder. The only person who could have the speed and annoying guts to push me over is only one person, he thought angrily as he tried catching the other blur.

"Sonic!" he hissed as he saw the other blur "oh-ho! Think you can fight me huh? Well lucky for you I don't have time to wipe you face all over the place! Hey that rhymes!" Shadow felt his anger rise at the challenging insult. "You're dead faker"

"You still call him that? Heh this was definitely the wrong time anyway my stop is here" the blur halted right in front of the Vault in the hall, shadow tried stopping but he knew he'd pass by before stopping and as he past the figure he met a feral golden eye. "Who?" the figure smirked and tripped the black hedgehog, shadow hit the ground hard and his vision was blurred.

"Shadow, Shadow are you ok?" he was pulled up again and rocked dizzily on his feet, pain stung at his legs from the suddenly loss of velocity. "You know you way a tone!" he looked at rouge who brushing his arm off, he was pulled his arm away and flinched in pain as he turned around. "What?"

The vault was destroyed, he walked over to the destroyed vault door and frowned. "What the, nothings gone?" rouge scoffed, shadow walked in and stumbled a few steps rouge had a grip on his shoulder so he wouldn't fall. "I'm fine let go" he shook her hand off, he sighed "of course you are" they searched around for anything missing. "Wait" he stood up from a pile of coins and closed his eyes. It wasn't in here...I had it, he thought trying to sense any chaos energy but there was no sign.

"What is it?" rouge was now beside him looking at him sideways, he growled lowly. "He stole my chaos emerald"

Rouge gave him a lop sided grin, "what? Who stole your emerald" shadow looked down and noticed something tucked in his glove, he pulled out a piece of paper folded under his black wrist band. He unfolded the note and red it.

'Your time is short master of chaos' he crushed the piece of paper he felt his spines prick up. "That hedgehog has just written his death sentence." He turned around rouge stopped him, the commander and two grunts were standing behind her.

"Agent shadow" Shadow could feel the anger boiling in his body, the commander sighed. "Bring him in, Shadow"

"What?" shadow showed confusion but shook it off and crossed his arms, rouge on the other hand kept her confusion. "Capture sonic and bring him in...Alive please" The commander watched the hedgehog as he frowned, his ears slanted forward showing his dislike to the plan. "Understood?"

"Yes Commander I'll leave immediately"


	2. chasing the wind

Chasing the wind

"When can I go?" shadow and rouge were in one of the scout helicopters, the hedgehog got looks from all six passengers strapped in the seats. They had left immediately after the base attack, the commander had gotten Intel that sonic was sighted near new-Westopolis and the president was also curious to know what was going on so it was killing two birds with one stone, and they'd check the town for the blue speedster then go inform the president of the progress.

Rouge sighed, "can you just chill for a minute? We're almost there" shadow frowned staring out at the bottom rotating propellers of the helicopter. "If I had gone alone I'd be there by now this is taking forever" he mumbled low enough so that the soldiers wouldn't hear, Rouge turned around to look at the only passenger standing, the dark hedgehog looked at her for a brief second then out the window again.

"I know your worried about omega but we have to get your emerald back to find him quicker, you know that" Shadow's gaze dropped to her and she nodded. "Plus omega's a tough cookie, so don't worry" she patted her partner's hand; he nodded slightly at the effort of comforting him.

"Alert, Alert target has been spotted" shadow almost smiled as he turned to the two drivers in the front of the copter. "Where?" shadow asked looking at them, the left driver gave shadow what looked like a large mirror.

"Don't know for sure seems the wasp has spotted him, take a look see" the pilot pressed one of the three red buttons on the circular mirror. An image appeared of a blur of a path way and grass on each side the path was cracked water was spraying from certain holes. Then there was the target, sonic the hedgehog was riding along the sprays of water on a skate board then the path ahead cracked even more only to have knuckles pop out of the middle with his fists up.

"Open the doors" shadow stated giving the pilot the mirror, he hesitated "But...We haven't reached the city yet" shadow glared at him baring his fangs timidly. "Open the door or I'll tear it off"

The sides of the chopper opened gust of wind flew in along with the deafening roar of the propellers; shadow trotted to one side and looked down. "Shadow, Are you crazy! Be careful" Rouge yelled, she unstrapped her seatbelt and stood next to shadow. He glanced at her then jumped out the helicopter far enough not to hit the bottom propellers of the transport, he landed in a crouch then looked up there was nothing but desert all around in the distance he could see the walls of the city. "Shadow I'll meet you there go due north I'm sure you can see it" Rouge's voice came from his communicator. "Right" he huffed and began skating towards the city.

When he reached the outer limits of the city he noticed a guard post the officer was waving a stop sign high in the air, shadow frowned and began speeding up. In response the officer got in front of the entrance, the speeding hedgehog growled "I don't have time for this" he used his own chaos energy and disappeared in a flash of green reappearing on the other side of the entrance.

He could hear gun shots and missiles being fired, he ran towards the noise he was headed for the park gate when he noticed something flying in over the parks wall.

"You've got to be joking, when did he learn to fly?" Rouge laughed from the communicator, shadow growled. "Where's the wasp?"

"Right behind him...It" There was a large explosion in the distance. "Never mind"

He looked at the glass building he stood next to, he chaos controlled up to the top of the building. Everything was lighting up in the city now that the moon was out he squinted his eyes and searched the roof tops for his run away target. "Shadow he's here"

The hedgehog turned the G.U.N. helicopter was following something in the distance. Shadow used chaos control and got closer, the helicopter was following Sonic.

"What's up with them is Shadow out tarnishing my good name again?" he growled at this and started perusing from the opposite side of where sonic was, he gathered his energy and shot a chaos spear his doubles path. "Very unlikely"

Sonic looked over but kept running.

"Hey you're after me to?" Shadow watched as the blue hedgehog ring dashed to another building and was now running along the windows. "The commander has asked me to bring you to him" Shadow hissed as he kept along the opposite roof.

"I see well sorry I don't want to, besides this is a blast" Shadow lost sight of his target as it jumped into one of the buildings he growled, and jumped using his shoes to propel himself to a higher ledge. Sonic burst through a window down bellow grabbed a flag pole and was wall jumping back and forth up the building till he was on a ledge a little higher up then shadows and was running again.

"Well I must bring you to him" The blue hedgehog looked across at him then waved as he began speeding up. "I won't fail, he said I had to bring you in alive but not conscience" Shadow couldn't help let a smirk cross his face then he concentrated disappearing from the roof he reappeared on the highest building it was a tower looking above the whole city, he looked around till he spotted sonic.

"Chaos spear" he mumbled as he shot multiple shots at the speeding creature, "time is short" Shadow closed his eyes as he continued shooting the spears. "For you"

His mind suddenly became blank as he felt chaos energy flow from everywhere he shivered at the feeling.

"YO!" His eyes sprung open as Sonic ran up at him, Shadow felt the rush of wind lost his balance and fell backward. "Damn it, what was that" he activated his shoes to hover and slowly lowered. "Aren't you going the wrong way?"

He felt someone grab his hand and he was now going up, Rouge was bringing him up to the helicopter that was now aligned with the top of the building shining a search light at the blue speedster standing on the top.

"Throw me" he hissed pointing at the building, rouge smiled and did as he asked tossing the black creature at the building. He landed against it on his feet and pushed up landing on the side on the copter, then pushed again.

Sonic seemed to have red his motive and was already jumping back, they were both falling. "Have a juice in me friend" Shadow looked at Sonic just in time to see him spin dashing towards him he was hit hard through the window of the building.

He pushed himself up and looked out the shattered window, Sonic was gone leaving but a trail of wind.


	3. meeting faces

Meeting faces

Shadow held his head as it rang from the impact; he stood in the broken window looking down at where sonic had once been. "I'll get you faker"

"Shadow, Hey shadow where are you?" rouge flew by the window as she called his name, the hedgehog rolled his eyes. "Up here rouge" he huffed; she stopped at the answer and turned around now spotting her partner.

"He got away?" shadow frowned as she landed in front of him, she smiled. "It's ok"

"No it's not..." he spat at her angrily, she was expecting the reply and was still smiling. "Well come on, the president is waiting." Shadow shook off and looked out the window, without a second thought he jumped from the building with rouge close behind him. He activated his shoes right before landing in the empty pathway. "Which way?" he asked her looking up at the bat that hovered above him; she pointed to her left down the street.

He sped down the street towards the now visible town hall; it was a big gray building with several flags above the front door. He got to the door and waited till rouge caught up; she landed neatly next to him and nodded. "Ok let's go"

They entered the large doors and looked around. The interior was very bright coloured two stair cases led up from both sides of the room with a statue in between of a warrior with a shield and sword, above the roof had more flags hanging along with a large glass chandelier. "ah shadow, rouge I've been waiting" they looked up the president was walking down to them as he greeted them both with a handshake which rouge took gladly, shadow stared at his hand hesitantly before doing the same. The president was one of the only people around who admired his company besides the commander who shadow himself respected and the commander in turn did the same.

"come Let us sit in the visitors quarters" he led them to another room off to the right it had a fireplace several couches, a large wooden table and a huge window showing the street the two had come down to reach this place. They sat down and stared in silence before the president cleared his throat to begin.

"I understand that E-123 Omega has malfunctioned somewhat and attacked troops, but what exactly were they supposed to look for in the cave? And who attacked HQ?" shadow saw rouge move uncomfortably in her seat; he sighed and looked at the president. "It was supposed to be recon to deal with the trouble that a small town nearby said was there, and Omega was sent to keep an eye on things. That's about all we know about that, and the one who attacked head quarters was that annoying pest sonic he stole my chaos emerald."

The president seemed unhappy with this answer, and shadow hated that he had to explain everything.

"So, what is the plan then?" The president stated more then asked looking over to the door they entered, Shadow followed his gaze, "Commander?"

The commander walked closer with his hands behind his back he looked at rouge then shadow who quickly diverted his gaze. "I take it you failed?" Shadow glared at him with his ears down. "No, I will catch him he won't get away from me a second time"

The commander chuckled slightly. "Are you sure? It seems he's not being hunted by just us"

Shadow sneered and waved a hand in front of his face and closing it into a fist. "He will by captured by me, I won't allow him to escape my grasp again"

"Alright, you two report to HQ we will continue this in the morning." Shadow shook his head. "No, I know where he is and if I ait all night he'll be gone" The president leaned back and exchanged a glance with the commander. "Alright shadow, but I will be accompanying you this time" Shadow stared at the commander for a second before closing his eyes and standing up.

Rouge got up and followed shadow that walked past the commander and out the door.

"Commander Keep an eye on shadow and rouge" The president ordered when he knew the two were out of ear shot, the elder man looked at him. "Yes Mr. President I plan to, with Omega on the loose there's no telling what will happen to them. And shadow and rouge both seem rebellious at the moment not that shadow never was but this situation isn't helping us gain his trust anymore than before."

The president nodded and looked out the window at the black arms hybrid he was walking towards the street but rouge stopped him and was talking to him. "Yes keep trying; I want him to trust us"

"shadow stop wait for the commander" rouge pleaded to the hedgehog who was giving her a death glare as she blocked his passage, "I don't need That man to follow me everywhere I go!" he practically yelled making her shrink slightly.

"Well like it or not I'm going with you" Shadow turned to face the commander who was walking up to him, he turned back and began to go down the street lit by lamps. The three walked for about twenty minutes before reaching one of the gates that lead out of the city to the desert like terrain outside. "He's out there I can sense a chaos emerald a few clicks from here." He pointed in a direction and looked at the commander who nodded to continue. They walked out into the wasteland searching around for any clues of where sonic may be shadow looked from a large rock the commander was under him and rouge was searching from the sky.

"You know shadow, the president is fond of your company" The commander began as he looked and the black creature, shadow gave him a careless look. "I know, but it's just hard to trust after so many betrayals" he looked at the ground with a sad look but perked up when rouge called to them, they went towards her and stopped she was tugging on two legs protruding from the ground.

"Shadow come and help knucklehead he's stuck in the hole" he sighed walking over to the echidna's legs he grabbed one leg and pulled him right out tossing him to the ground. "Ow...huh shadow rouge?"

Knuckles sat up and shook his head, rouge laughed at the red mobian. "So why were you in a hole?"

"Oh, me and sonic were...Sonic!?" he looked around and punched the ground. "He left me here!" shadow glared at him. "Where is he?"

"He must have gone after that ghost! Man when I get my hands on him he's" Rouge saw that shadow was losing patience and fast. "Knuckles focus here, which way did he go?" Knuckles glared at her and stood up. "How would I know bat girl! I was in a hole!"

"He's in there" shadow interrupted pointing to a cave a little ways away, rouge looked in the direction. "How do you know?"

"I can sense a chaos emerald in their"


End file.
